args = parser.parse_args() do = os.system cd = os.chdir with open('commandline_args.txt', 'a') as f: f.write(' '.join(sys.argv)) f.write('\n') # simulation_platform = "CPU" # OpenCL, CUDA, CPU, or Reference # simulation_platform = "OpenCL" simulation_platform = args.platform platform = Platform.getPlatformByName(simulation_platform) if simulation_platform == "CPU": if args.thread != -1: platform.setPropertyDefaultValue("Threads", str(args.thread)) print( f"{simulation_platform}: {platform.getPropertyDefaultValue('Threads')} threads" ) proteinName = pdb_id = args.protein chain = args.chain.upper() pdb = f"{pdb_id}.pdb" if chain == "-1": chain = getAllChains("crystal_structure.pdb") print("Chains to simulate: ", chain) if args.to != "./": os.system(f"mkdir -p {args.to}") # os.system(f"cp {pdb} {args.to}/{pdb}")
args = parser.parse_args() do = os.system cd = os.chdir with open('commandline_args.txt', 'a') as f: f.write(' '.join(sys.argv)) f.write('\n') simulation_platform = "CPU" # OpenCL, CUDA, CPU, or Reference simulation_platform = "OpenCL" platform = Platform.getPlatformByName(simulation_platform) if simulation_platform == "CPU": platform.setPropertyDefaultValue("Threads", "1") print(f"{simulation_platform}: {platform.getPropertyDefaultValue('Threads')} threads") proteinName = pdb_id = args.protein chain=args.chain.upper() pdb = f"{pdb_id}.pdb" if chain == "-1": chain = getAllChains("crystal_structure.pdb") print("Chains to simulate: ", chain) input_pdb_filename, cleaned_pdb_filename = prepare_pdb(pdb, chain) ensure_atom_order(input_pdb_filename) getSeqFromCleanPdb(input_pdb_filename, chains=chain)